Gotta Catch 'em All: Pokemod!
Elemental Forums
The first mod I ever did was to replace all the soul crystals in Morrowind with pokeballs. I wanted to do something more ambitious, but I barely figured out how to model pokeballs and it was just too daunting to mod all the objects in Morrowind (buildings, trees, all the NPCs; it would be a huge task to make that game resemble Pokemon). With Elemental, it just might be possible to do a full-on Pokemon total conversion.
Simple first mod: Change the summon spell icons to look like pokeballs, and then add an "I choose you!" sound to the casting effect.
Incremental mods:
1. Model various pokemon and put them into the game. At the time I was playing Morrowind, I found a website where someone had posted dozens of pokemon renders he'd created; but I was never able to get in contact with him. There may be people who have made pokemon models and would share them. Since these are low-poly graphics, it shouldn't be too hard to model them from scratch; the rigging and animation is what concerns me. It may be possible to use the bones and animations of creatures already in-game. Finished pokemon creatures could be further modded into generic dragons, turtles, plant monsters, and whatnot, so they'd have value outside the Pokemon fan community, LOL.
2. Model (or create in the tile editors) structures that resemble those of the pokemon cartoon and games. Pokemon's art style is simple and boxy, so it shouldn't be too hard.
3. Script pokemon-themed quests.
4. Model pokemon hairstyles and body shapes. Ash, Misty, Nurse Jenny, Professor Oak; characters with a distinctive hairstyle would serve as reference for the hair models, which would be useful in themselves to other, non-pokemon, modders. Body shapes would be more difficult, since there's only one real body style each for male and female units. Maybe just tweak those meshes to look more anime-like. (May not be able to do much with proportions because of the rigging.)
Big, game-changing, mods:
1. Create a system by which monsters, but not humans, can be captured in pokeballs and later released, as charmed units, which can then be recaptured.
2. Replace the magic and essence system with something else, something plausible in the Pokemon world.
a. Maybe somehow require the presence of a unit on the tactical combat map in order to cast certain spells. So, you could learn charizard's special ability (a spell), but you could only use it when charizard is in play. Or, when on the world map, you can only cast certain spells if a given pokemon is in your sovereign's army.
3. Establish sovereigns and champions as non-combatants.
4. Eliminate the ability to found and manage towns, yet keep towns interesting.
a. Fixed world map modeled after Pokemon Yellow?
b. It would be cool if you could click on a building to access it. So, for example, only certain towns would have a gym, whose leader you could challenge; and others would have Pokemarts, pokemon nursing stations, pokemon breeders, and so on.
5. Completely redo the tech tree.
6. Completely re-write the diplomacy screens and interactions. You would no longer recruit adventurers, but instead talk to them or challenge them to pokemon battles.
7. Make multiplayer work, and make it interesting. Maybe multiplayer could be a race to become the #1 pokemon trainer by earning all the badges and winning the big tournament. One can only achieve that by a) defeating all the other trainers, 
finding certain special items and pokemon, c) developing trainer skill (magic and technology research), and possibly d) completing a "master quest" (such as filling out Professor Oak's complete Pokedex).
These "big, game-changing, mods" may be too much. If the interest is there, and if a large community develops around the idea, and if some of them know hardcore programming, it could be done. Alternatively, the conversion could follow a tongue-in-cheek "War of Pokemon" theme. The intro screen would explain that pokemon, once used for peaceful purposes by skilled trainers in competition, are now used for war. The game casts you in the role of one pokemon trainer dedicated to conquering the Pokemon World.
But take my offer with a grain of salt, as me is busy >.< Again, good luck with however far you take this.
I'm kinda unfamiliar with Pokemon rules so i'm not sure. I think i saw 2-3 anime episodes, and i saw some pokemon cards when i played tabletop MtG, that's all. But if it's something like Gladius then it should be fun.